My main character's name is taken from someone I know. I don't know him well, but know relatives and friend's of his well. I've contacted him to let him know and as a courtesy ask if he minds. The character bears no real resemblance to the real man. Unless the name is trademarked there is no need for permission, and most people I know don't trademark their names.
How would you feel if a contact of yours used your (unique) name as a character in a book? I think I would feel pretty honored, even if the character is a scumbag, but with a common name like mine the odds of it happening are pretty slim. Even just my last name, the only Matthews I can recall in book, film or tv is the boy from Boy Meets World. Not quite The Grapes of Wrath there.
I have also used the name of a friend, a former roommate for a short time in California from years ago, who recently passed away. He was a strong personality and a great person. I used his name to honor him for a very strong character who had seen adversity and shared some of the real interests of the real man.
Creating a character that is believable is difficult. You can make them too perfect or too imperfect very easily, or just too boring or too hard to believe they are real. A big part of that is the name. Everyone in the world isn't named John, Tom, Robert, James, Mary, Lisa, Becky, etc. But obviously many are. So a good mix of more common names with some unique ones thrown in help give the whole work more plausibility, I believe. As a 'John' I come across many others named 'John' in real life but naming two characters in a book the same name could be quite confusing, unless done for comedic value then if done right could have good effect.